Alignments for a candidate for prpE in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Echinicola vietnamensis KMM 6221, DSM 17526

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Echvi_1268 Echvi_1268 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Cola:Echvi_1268
          Length = 632

 Score =  712 bits (1839), Expect = 0.0
 Identities = 344/618 (55%), Positives = 439/618 (71%), Gaps = 6/618 (0%)

Query: 28  YQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLDRHLQ 87
           YQ+S+  P+ FW        W K + KV    F   +V  KW+ +G +N+  N L+RHL 
Sbjct: 15  YQKSVTEPEQFWARIADSFHWKKRWDKVLEWDFEGPDV--KWFVNGKVNITENILERHLF 72

Query: 88  ENGDRTAIIWEGDDASQS-KHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMVPEAA 146
             GDR AIIWE +D ++  + ++Y++L+ +VC+F+N L   GI KGD V IYMPMVPEAA
Sbjct: 73  IMGDRPAIIWEPNDPNEEGRTLTYRQLYHEVCKFSNALKAKGIGKGDKVIIYMPMVPEAA 132

Query: 147 VAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKNVDDAL 206
           +AMLACARIGAVHSV+F GFS  A+A RI D  ++ V+TSD   R  + I +K  VD+AL
Sbjct: 133 IAMLACARIGAVHSVVFAGFSSSALADRINDCEAKAVLTSDGNFRGTKKIAVKDLVDEAL 192

Query: 207 KNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLFILYTSG 266
           +     ++E V+V +RT  ++   EGRD+WWHD ++   D ++AE M++ED LFILYTSG
Sbjct: 193 EKTK--TIETVIVYQRTKQEVKMVEGRDIWWHDAIDGQPDTNEAEVMDSEDMLFILYTSG 250

Query: 267 STGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLACGAT 326
           STGKPKGV+HTTGGY+VY+  TF+ VF Y PGD+YWCTAD+GW+TGHSY++YGPL  GAT
Sbjct: 251 STGKPKGVVHTTGGYMVYSKYTFENVFQYSPGDVYWCTADIGWITGHSYIVYGPLLAGAT 310

Query: 327 TLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRILGSV 386
           ++MFEGVP +P   R   +VDK+QVN  YTAPTAIRAL A G K IE     SL++LGSV
Sbjct: 311 SIMFEGVPTYPDAGRFWAIVDKYQVNQFYTAPTAIRALEAHGTKPIEPYKLDSLKVLGSV 370

Query: 387 GEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRPFFGVQP 446
           GEPIN EAW WY   +G  +CP+VDTWWQTETGG M++P+ G T  K   AT P  GVQ 
Sbjct: 371 GEPINEEAWHWYHTHVGKNRCPIVDTWWQTETGGIMVSPIAGITPNKPAYATMPLPGVQL 430

Query: 447 ALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRD 505
           A+VD EG  L+G A EG+L I   WPG  RT +GDH+R +QTYFS +  MYF+GDG +RD
Sbjct: 431 AIVDPEGKELKGKAVEGNLCIKFPWPGMLRTTYGDHDRCKQTYFSAYPGMYFTGDGVKRD 490

Query: 506 EDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYAYVTL 565
            DGYY I GRVDDV+NVSGHR+GTAEIE+A+  HPK+ E+AVVG PH +KGQ IYAYV  
Sbjct: 491 HDGYYRILGRVDDVINVSGHRMGTAEIENAINEHPKVIESAVVGYPHEVKGQGIYAYVIC 550

Query: 566 NHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDTSN 625
           +        L  E+++ + K IGP+A PD +     LPKTRSGKIMRRILRK+A G   N
Sbjct: 551 DLKNRTEENLIGEIKDTITKSIGPIAKPDKIQIVPGLPKTRSGKIMRRILRKVAEGSFDN 610

Query: 626 LGDTSTLADPGVVEKLLE 643
           +GDTSTL DP VVE+++E
Sbjct: 611 MGDTSTLLDPAVVEEIIE 628


Lambda     K      H
   0.317    0.135    0.421 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1299
Number of extensions: 72
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 652
Length of database: 632
Length adjustment: 38
Effective length of query: 614
Effective length of database: 594
Effective search space:   364716
Effective search space used:   364716
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources